Some Genes Are Less Helpful than Others

In an international collaboration published in Nature, researchers have identified people with natural gene-disrupting mutations – who have a gene that has been naturally “knocked out” – and systematically studied the biological consequences. The project provides a framework for using naturally-occurring genetic variation to gain valuable insights into how individual genes affect health and disease.

All people carry two versions of almost every gene in their genome, one from their mother and one from their father, so that even if one version is disrupted, there is still one working version. But, occasionally, a child can inherit disruptions in both versions of the same gene, meaning that they have no working copy of the gene. Researchers from the University of Cambridge, Wellcome TrustSanger Institute, Broad Institute of MIT and Harvard, University of Pennsylvania (UPenn), and the Center for Non-Communicable Diseases in Pakistan analysed a cohort of more than 10,000 people and found more than 1,300 individual genes that were completely knocked out in at least one person. People with these natural knockouts reveal what happens when there is complete loss of a gene’s function, providing valuable insights into the role of the disrupted gene.

“To determine what a gene does, traditionally scientists ‘delete’ it in a mouse or a zebrafish and observe what happens. However, due to species differences, findings based on such experiments cannot always be extrapolated to humans. In contrast, this study leverages the high degree of consanguinity (relatedness) in Pakistan to find naturally-occurring gene knock-outs with direct relevance to human health and disease.”

Professor John Danesh, along with the paper’s first author Danish Saleheen, led the assembly of a cohort in Pakistan to study the genetic risk of heart disease. In the sequence data from the first few thousand participants, the researchers noted a large number of naturally knocked-out genes, and pivoted to study the consequences of these genetic variations.

Previous human cohort studies have generated lists of potentially disrupted genes in participants, but the team went a step further in the current study, correlating the nonfunctional genes with the physiological measurements. Within the cohort, the researchers found 1,317 genes where at least one person had both of their copies disrupted. Roughly a third of these disrupted genes existed in two or more people, allowing for further analysis, and the team determined that seven of the disrupted genes were associated with at least one of the measured traits.

“The Human Genome Project revealed the genetic blueprint for human life, but we’re now entering a new era in genetics where we can systematically examine what it means for humans when parts of this blueprint are missing. This has been made possible by advances in DNA sequencing technology and analytical capabilities to deal with the avalanche of data produced, combined with access to people who naturally lack functioning copies of particular genes.”

Most notable was a family that had two disrupted copies of the gene APOC3. The research team returned to this family for clinical evaluation and found that those family members without a working version of APOC3 cleared dietary fat from their blood at a faster rate than other relatives could with one or two functional APOC3 genes. The natural power of APOC3-disrupting mutations to lower this risk factor for heart disease could be a boon for preventative therapies, following the roadmap laid out by study of a different gene called PCSK9.

Studying people with naturally occuring disrupted genes can help guide drug development, by mimicking the effects of a drug that blocks the protein made by that gene. For example, in 2005, a group of researchers reported that a nonfunctional version of PCSK9 was associated with lower blood cholesterol, and a year later, researchers described an adult woman with two non-functional copies of PCSK9 — indicating that humans could tolerate complete loss of this gene. Such observations eventually led to the development of medications that block the PCSK9 protein, and these medications are now approved by the U.S. Food and Drug Administration to lower blood LDLcholesterol.

“This research provides a framework that could be scaled up to establish a global ‘human knockout’ project: scouring populations for humans with naturally-occurring knockout mutations, and determining the range of physical consequences stemming from that gene-function loss to better understand the genome.”

Dr Pradeep Natarajan, a postdoctoral research fellow in Sekar Kathiresan’s laboratory at the Broad Institute and co-first author of the study